1

Mapping the Location and Biodiversity of Eelgrass (Zostera marina) in the

Fal Estuary

Lewis Chaffe, FdSc Marine Science

University of Plymouth,

Falmouth Marine School,

Falmouth,

Cornwall, UK

TR11 3QS

Submitted May 03rd 2012

lewis_chaffe@hotmail.com

079846 472448

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Abstract

Mapping the location and biodiversity of eelgrass (Zostera marina) in the Fal estuary is an

important issue, due to the nature of eelgrass to fragment and relocate at signs of stress.

Keeping up to date with the fluctuation in the size of the eelgrass beds provides needed

information for local authorities regarding the potential harm of building and recreational

activities. The survey relied on the use of certain pieces of equipment, the Scubar, the

Photo-quadrat and the Aqua-scope as well as the use of GIS mapping software. Together

they provide an accurate view of the current state of the eelgrass beds in the Fal estuary.

The data was hard to come by since the conditions were rarely favourable for boat drift

surveys and underwater surveys, and the biodiversity was hard to measure due to the

seasonal temperature changes. It is evident that maerl is present outside of the reference

zone and eelgrass doesn’t extend as far into the reference zone as previously thought, but

has is largely found on the outside.

Keywords

Eelgrass, Fal estuary, Biodiversity, Mapping, Zostera marina.

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Introduction

The Fal estuary is the country’s largest estuary as well as being the world’s third largest

deep-water port. It brings in trade and tourism to the surrounding areas as well as hosting

an array of different species. The Fal is also home to eelgrass, Zostera marina, a grass like

plant that is found on the sea-floor. It provides a habitat for fish, shellfish and seahorses to

thrive, protected from predators and with a ready supply of food.

In the course of this project, the aim is to find and map the locations and distribution of

eelgrass in the Fal estuary. A topical issue as currently the Falmouth Harbour Commissioners

(FHC) are seeking to expand the dock which will provide jobs and revenue to the

surrounding area. The problem arises if or when eelgrass is found near the location of the

dock, should the economic value of the dock be compromised to protect a small amount of

eelgrass and its inhabitants? The expansion of the dock also requires significant deepening

of the channel through dredging, a process which could prove detrimental to nearby

eelgrass habitats. Development in Falmouth is torn between meeting with urban

development plans prioritizing coastal development, including the harbour, as well as

regional development plans set by Cornwall County Council to prioritise environmental

sustainability (Cornwall County Council, 2005; Dinwoodie et al., 2011). The Fal estuary is a

valuable habitat encompassing SACs (Special Areas of Conservation), AONBs (Areas of

Outstanding Natural Beauty) and SSSIs (Sites of Special Scientific Interest); because of this

the local council has a responsibility to ensure the protection and conservation of the Fal.

The FHC has commissioned this project to locate the extent of eelgrass in the proposed

reference zone as well as the species diversity of the eelgrass beds that may be affected by

potential construction; this information should be able to provide adequate insight into

resolving the issue to benefit both sides.

The Fal estuary is a sheltered ria system and owes its rich biodiversity to the many different

habitats and substrata that exist within it (Hagger et al., 2009). The local human impacts

have caused past troubles including large mining outbursts of heavy metal contaminated

water at Wheal Jane, 1992 (Younger et al. 2005). Outbursts such as this have encouraged

certain adaptations in the local wildlife to deal with large changes in stress, such as surviving

in an area with changing salinity levels where the inland freshwater mixes with the English

Channel (Langston et al., 2006). Dredging in the Fal may affect eelgrass beds directly and

indirectly. Apart from the obvious damage to eelgrass beds via physical removal from

dredging, it is also shown to cause indirect reductions in surrounding eelgrass habitats

(Sabol et al., 2005). It has been shown that the increased turbidity and sedimentation

caused by dredging leads to loss of eelgrass vegetation due to the amount of stress the sea

grasses can survive for the period of time until the water returns to a normal state

(Erftemeijer et al., 2006).

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Eelgrass beds are highly productive areas providing breeding and nursery grounds, they also

provide a key role in stabilizing the sediment and surrounding substrata (Duarte, C. M.,

2002). The indirect loss of eelgrass is also attributed to the loss of water clarity, which would

affect the amount of light available to the photosynthetic grass, and nutrient loading which

increases phytoplankton growth affecting light penetration (Walker et al., 1992). The

dredging in the Fal estuary may exclude or not directly remove some eelgrass beds but the

indirect effects may lead to the eelgrass beds that are left shrinking or fragmenting.

Fragmentation results in habitat loss, as the eelgrass is removed from the area there is less

protection for fauna in the area. The loss of eelgrass would also affect the surrounding

sediment, without the structural support provided by eelgrass beds the sediment would

become loose and could lead to erosion (Bell et al., 2001). A study concerning the dredging

effects on eelgrass (Sabol et al, 2005) used hydro acoustic techniques to map eelgrass beds

before and after dredging alongside a bed that wasn’t dredged. Their results came back

showing significant reason to believe that year-to-year variation of eelgrass coverage,

fluctuations in growth, changed almost as much as dredged sites. The results also show

natural eelgrass relocations from deeper waters, usually, to more shallow waters which

could identify a need for more light due to declining water quality. Due to the dredging, and

relocation of what vegetation remained, the dredged area remained largely uninhabited

during subsequent surveys. Another survey (Neckles et al, 2005) showed similar data stating

that, with favorable conditions, the eelgrass beds would recover in 6 to 20 years. Duarte

(2002) suggests that with current sea grass losses and human pressure on the shoreline the

positive effects of legislation and conservation won’t outweigh the negative impacts, which

could lead to irreversible loss of sea grass, a habitat which accounts for 0.2% of the global

ocean coverage.

The dredging in the Fal estuary could lead to similar levels of fragmentation, indirect loss of

some of the habitat or potentially natural relocation. Potentially eelgrass could spawn and

relocate to less convenient places. The fragmentation and relocation of eelgrass beds could

help explain why recent surveys of the Fal estuary (Pollitt, C., 2011) haven’t shown results

where previous maps showed eelgrass, and why results have shown beds where there

previously were none. There are other causes to loss of eelgrass besides dredging and

natural variations. Major losses of habitat can be attributed to damage from boats such as

propellers, mooring and anchor damage (Reed, B. J., 2006).

Mapping eelgrass proves difficult, as with any marine flora, it raises a need for a

measurement system that penetrates the sea’s surface. There are two main considerations

when looking for a method or system to map eelgrass: the size of the survey area and the

required level of detail. A large scale survey can’t use the same level of detail as a small

survey site; it is, as well as the costs, impractical (Precision Identification, 2002). There are

two main groups of systems or methods to map eelgrass, remote and in situ. Remote

mapping is simply “acquiring data about an object without touching it” (Hughes, S., no

date), it uses a range of systems such as radar, satellite and infra-red. It is usually used to

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provide data on a large survey area. In situ mapping is a more ‘hands-on’ approach; the

survey is usually carried out by someone in the field. It is a useful and a cost-effective way to

survey small areas this way, if you have the man-hours. It may be necessary to combine the

two methods, using remote mapping to quickly survey a large area and then surveying a

smaller amount in situ. Satellite sensors can be used to record chlorophyll levels close to the

surface, results would indicate percentage coverage and density of chlorophytes. Airborne

sensors, such as aerial photographs/video imagery, can be used to produce more specific

results at a smaller scale. Hydro acoustic sensors, such as those used in studies by Sabol

(2005), can produce very accurate sonar images of seabed bathymetry, texture and

coverage. Techniques for smaller areas of eelgrass beds would involve the use of SCUBAR;

an extendable underwater camera, an ROV; a Remote Operated Vehicle, or removal by

divers, grab and core samples. It is best when mapping to complement one method of

mapping with the other, utilizing satellite imaging or aerial photos and then providing

additional data with samples (Precision Identification, 2002).

Previous studies mapping eelgrass (Precision Identification, 2004; Godet et al., 2008;

Costello et al., 2009) all profess that the best technique for mapping eelgrass is based upon

aerial photography, digital imagery and ground truth variation. The combination of these

three things covers most factors such as size, depth, percentage coverage and for additional

detail samples could be taken for analysis. Due to the surge in satellite mapping recently,

satellite images of the Fal estuary are easily accessible. Aerial photographs are also readily

available, although they are less commonly used due to the advancements in satellite

imaging. Because of the wide-scale use of these methods and the accurate results

accredited to them, they should be adopted for use in current research projects.

The current plan is to survey as much of the Fal estuary as can be done with special

attention paid to the reference zone. The reference zone is a 500 m² plot of marine land set

apart to protect the diverse benthos that is located in the estuary (Bennett, O., 2011). This

reference zone mostly covers beds of maerl as well as a small portion of the Fal's eelgrass

habitat. A variety of surveying techniques will be utilised to map the eelgrass beds. The live

feed from the Scubar, an underwater camera, will be positioned alongside a Global

Positioning System (GPS) on a monitor providing live and accurate updates about where the

eelgrass borders lie. This will be placed in a Geographic Information System (GIS) map

alongside current and previous knowledge of the eelgrass beds, hopefully showing if there is

growth, loss or even a lack of knowledge of eelgrass beds. Another piece of equipment, the

photo-quadrat, will be used to study and view the different species that reside in the

eelgrass beds.

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Photo-quadrat

The Photo-quadrat is a large metal frame with a mount for an underwater camera on one

end and a quadrat (50mm x 50mm) on the other. It allows you to sample the seabed using

quadrats from the safety of your boat.

It’s a very straight-forward piece of equipment. Attach your underwater camera or a camera

in an underwater case to the mount, and a rope to the top so you can lower it down. You

then alter the zoom on the camera so that it fits in the quadrat. Set your camera to video

and start filming as you lower it slowly to the seabed. The foam tubes on the ropes should

ensure that the ropes stay out of the camera’s view. Leave the photo-quadrat on the seabed

for a few minutes until the dust settles, and then pull it up. Carefully pull it back onto the

boat and stop the recording. Place a damp towel over the camera to stop it from fogging up

due to condensation. The layout allows a quadrat survey to be conducted underwater, with

film or still photos. Wind, currents and drift will affect the placement of the photo-quadrat

so it is largely weather dependent.

SCUBAR

The SCUBAR is an underwater camera on an extendable pole; the camera produces a live-

feed of what it sees on a monitor on the boat, which can be recorded. It can be used to view

the seabed from the boat.

The SCUBAR kit consists of the telescopic pole, the camera, connecting cables and the

monitor. Connect the camera to the top end of the pole by releasing the latch, pushing in

the camera and replacing the latch. The cables attach to the other end of the pole and the

back of the monitor. Turn on the monitor using the red switch on the side and turn the

monitor on from standby, this will provide a picture on the monitor.

Aqua-Scope

The Aqua-scope is a large box with a glass bottom and a padded hole at the top. It mounts

onto the side of the boat and the bottom sits below the water line allowing you to see,

undisturbed, to the seabed.

Set-up is straightforward. There are two metal poles which hook under the boat and screw

on to the Aqua-scope. Once these are attached, secure the Aqua-scope to the boat using

rope as a precaution. Ensure that the bottom sits below the water line. Place your head into

the padded hole, and leave for your eyes to adjust. You should be able to see the seabed,

unless visibility is poor or the bed is too deep. The buoyancy of the box keeps it secured

under the boat, but it means that detachment is harder. Be sure not to lose the Aqua-scope

when you detach.

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Method

Equipment List

- A boat or survey vessel

- The Scubar and related equipment

- The Photo-quadrat; with rope

- A suitable camera (underwater or with underwater case)

- The Aqua-scope; with rope to secure it

- GPS; either handheld or as laptop software

- Laptop; with software (such as Chart Plotter), power source/adapter

- Standard safety equipment; including sensible clothing

- Recording equipment; lab-book, pen etc

Pre-plan an area to survey using maps, local knowledge and data. A chart plotter program

installed on a laptop would allow easy access to data and would save the course

automatically. Installing a screen capture program would allow the user to merge the data

into one video. Afterwards prepare the equipment needed and make sure to familiarise

yourself with it: equipment such as the Scubar, the Aqua scope and the Photo-quadrat.

Once on the boat, with the equipment secured, head towards the survey area, making sure

to take GPS coordinates.

Prepare the Scubar for use, attaching the cable to the laptop. This allows better quality

videos and a larger storage capacity. Make sure to take into account wind direction when

preparing the transect survey; if possible use the wind to drift across the proposed zone.

Lower the Scubar into the water until the bed is visible on the screen and then begin the

survey. The boat will probably move in the waves so the Scubar will need to be adjusted as

such and the wind and currents will probably push the boat off course, so small adjustments

will be required. This system of surveying works best with two or more people due to the

number of things that needs to be done simultaneously.

Once the survey is completed raise the Scubar, turn it off to conserve battery, and either

move on to the next survey site, head back into shore or prepare the photo-quadrat for use

on eelgrass beds found.

Using the boat, head to an area of eelgrass and then prepare the photo-quadrat by

attaching the camera and the rope. Lift the photo-quadrat over the edge of the boat and

slowly lower it down the seabed. Lower it slowly to avoid damaging the seabed, and make

sure to tie an end of the rope to the boat to avoid losing the photo-quadrat entirely.

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Leave the photo-quadrat on the seabed for a few minutes, for the dust to settle and a clear

picture to emerge. If you are taking still photos, you would now drop the weight to trigger

the camera. Raise the photo-quadrat and check the photo or film, looking to see if the

picture is clear and that the photo-quadrat didn't fall over on the bed.

The aqua-scope can also be used to take pictures and find locations of eelgrass beds, so long

as light penetrates down through the water column enough. It needs to be hooked to the

underside of the boat which can be tricky out on the boat due to the buoyancy of the aqua

scope. It should not, however, be deployed whilst in fast transit. To deploy the aqua-scope,

hook the two metal poles onto the rim of the boat, below the water surface. Then secure it

to the boat. Look through the hole to see the seabed and proceed to, slowly or through

drifting, transect the bed. Use the camera to take pictures or videos of the seabed.

Measuring the extent of the eelgrass bed will consist of transects, with the Scubar, into

shore from the estuary until the Scubar shows the presence of eelgrass. The GPS

coordinates of this point are recorded and this process is repeated until the eelgrass bed

ends.

The coordinates from these transects and photo-quadrat drops will then be inserted into

GIS mapping software on a map of past recorded eelgrass locations.

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Results

Photo-quadrat Sites

1 50N 10.27.12

005W 01.41.66

2 50N 10.26.71

005W 01.38.35

3 50N 10.27.05

005W 01.36.64

4 50N 10.28.88

005W 01.39.34

5 50N 10.29.30

005W 01.41.79

6 50N 10.28.88

005W 01.44.37

7 50N 10.30.47

005W 01.44.63

8 50N 10.30.47

005W 01.46.77

9 50N 10.29.74

005W 01.49.54

10 50N 10.24.63

005W 01.41.50

11 50N 10.24.83

005W 01.38.89

12 50N 10.25.22

005W 01.36.61

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Fig. 1 Photo-quadrat survey locations in the Fal estuary. (DigitalGlobe, 2012)

Fig. 2 First Drift Survey Transects. (Morley, R., 2012)

Red – Drift Transect

Orange – Indicate location of eelgrass

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Table. 1 Coordinates of Eelgrass bed border. (Chaffe, L., 2012)

Eelgrass Border x y

1 184578 33992

2 184577 34105

3 184570 34103

4 184575 34085

5 184582 34078

6 184577 34074

7 184586 34067

8 184580 34062

9 184585 34060

10 184581 34056

11 184584 34056

12 184582 34052

13 184583 34051

14 184580 34047

15 184582 34042

16 184579 34030

17 184582 34055

18 184579 34060

19 184580 34062

Fig. 3. GIS map of reference zone (red) and eelgrass bed border. (Chaffe, L., 2012)

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Analysis and Discussion

The extent of the eelgrass beds seen in the results shows what the current size is and location of the bed in the reference zone. It also shows that a large extent of the eelgrass bed is outside the reference zone and so unprotected by the relevant legislation. Due to its location and distance from the proposed dredging site it is unlikely for there to be very many direct detrimental effects, although increased sedimentation is still likely but unlikely to reach a level where stress will occur.

The second survey where the extent of the eelgrass bed was measured shows a slight variance to that of the first survey. The surveys were undertaken at different times of the year which could account for some loss as well as growth through natural seasonal responses. These fragmentations and growth would provide evidence that any adverse effect from dredging wouldn’t cause more loss than that of seasonal variation.

The photo-quadrats, although surveyed in an area where eelgrass was supposed to exist, proved unfruitful for the most part with only 4 videos showing any eelgrass at all. For the most part the quadrats return very little of anything, mostly dead algae’s and shells. There is also some presence of maerl in the photo-quadrats despite the survey taking place outside of the reference zone, which shows that some of the maerl bed is unprotected. Some of the still images taken from the videos prove difficult to analyse due to the presence of air bubbles, sediment kicked up by the photo-quadrat and dead algae obstructing the view.

The biodiversity of the eelgrass bed could be seemingly low due to the time, date and season of the survey as well as the presence of a boat and equipment. The timeframe of the survey would have fallen when most of the expected species may have died or left due to the changing climate, resulting in a false assumption of the biodiversity levels.

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Evaluation

The project could have been improved with an extended timeframe and more time available to survey. As it was the surveying was heavily dependent on both parties being free, the tides being right and the weather being such that the drift patterns weren’t too fast so the Scubar and photo-quadrat weren’t being dragged by the boat. As was discovered, moments where everything falls into place are few and far between.

Previous data on the eelgrass beds in the Fal were hard to understand, let alone plot into a GIS map which means that the previous data wasn’t as reliable or up to date as was expected. Because of this, the data and results weren’t as full or comparable as was first hoped rendering any statistical comparison moot.

GIS software also proved very difficult to use despite having the help and lessons provided for the software. What coordinate data that was used and translated into a GIS compatible format usually presented itself some distance away from the expected point, mostly inland.

If the survey were to be repeated, which is a must due to the constant changing and moving state of the eelgrass beds, it would be suggested that the surveys take place during the summer months at a period where the eelgrass beds are flourishing and biodiversity is high. Another survey should take place during winter to compare the loss of habitat due to changing temperatures. It is recommended that you not be dependent on other people due to the potential lack of availability during appropriate weather conditions. That being said having a partner or an extra pair of hands proves useful during the surveys due to the amount of things that need to be happening simultaneously, such as controlling the boat, controlling the Scubar, watching the monitor and recording the data.

Acknowledgments

This journal owes its completion to the work of Richard Morley, the supervision of Claire Eatock, Trudy Russell and Luke Marsh and the financial support of the Falmouth Harbour Commissioners.

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Appendices

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